Bio-1New developments of the geant4 Monte carlo simulation toolkit

TYL-FKPPL 2012, 28-30 May, Clermont-Fd, FranceTakashi Sasaki, Koichi Murakami KEK, JapanSatoshi Tanaka, Kuoko Hasegawa Ritsumeikan U., JapanAkinori Kimura Ashikaga Inst. Of Tech., Japan

Sbastien Incerti CENBG, France

Content*Bio-1 2011 collaboration activitiesDevelopment of specific applications at the Physics-Medicine interface PTSim software for particle therapy simulationDevelopment of specific applications at the Physics-Biology interface :the Geant4-DNA projectDevelopment of a new visualization schemeEfforts toward parallel Geant4Proposed workplan for 2012Collaboration matters

The Geant4 toolkit

The Geant4 toolkit: GEometry And Tracking 4*A set of libraries to simulate interactions of particles with matterInitiated by CERN in 1994 for HEP (LHC), successor of Geant3R&D 44 1994-1998, 1st release in December 1998Now developed by an international collaboration (~100 members)Object-oriented technologySet of libraries : not a user codeConstantly updated (two public releases per year)Entirely open source and free

Simulation of a particle physics experimentDefine a flexible geometryModel physical interactions : electromagnetic, hadronicGenerate primary particles and simulate their interactions Extract physical quantities and analyze them

CapabilitiesVisualizationInteractivityExtensibility

http://geant4.orgSLAC 2011

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PHYSICS-MEDICINEPTSIM

New particle therapy clinics are opening in JapanProton/Carbon-ion Facilities in Japan11 Proton/Carbon Therapy facilities in operation in Japan U. of Tsukuba PMRC (1983)NIRS (1979) (C)National Cancer Center East Hospital (1988)Shizuoka Cancer Center (2003)Wakasa wan energy research centerHyogo Ion Beam medical center (p/C) (2001)Fukui Prefectural Hospital (2011)Medipolis Medical Research Institute (2011)Southern TOHOKU Proton Therapy Center (2008)Gumma U. Heavy Ion Medical Center (2010)Quality life 21 Jyohoku (Under Construction) Nagoya CityU. of Hokkaido (Under Construction)*

PTSIM: Particle Therapy Simulation based on Geant4Project Development of a simulation framework for advanced radio-therapyFunded by the Japan Science and Technology Agency (JST) and Core Research for Evolutional Research and Technology (CREST)Oct. 2003 Mar. 2010Joint Project among Geant4 developers, physicists, and medical physicistsUse-cases were sampled from medical physicists at treatment facilities

*Software suite for simulating particle therapyGeometry DescriptionMaterial DefinitionOptimized Physics ProcessesScorersEvent Level Parallel ProcessinggMocren VisualizationMain ProgramUser interface commands(Input Macro File)DICOM HandlerPrimary BeamgMocrenDriverUse-case => Modularization => Provided as a class library KEK, TNCT, AIT, Rits, Naruto U.,NIRS, HIBMC, NCC

PTSIM in Radiation Treatment PlanningGRIDCLOUDSGenerally, simulation of 1 billion proton events need about 240 CPU hoursRTP completes dose calculation within 2 ~ 5 minutesLarge scale computing environmentis necessary*

PTSIM web interface*A PTSIM web interface has been developed to make easier for submitting jobs on Grid or Cloud

LCGNAREGI (Toyama NCT site)WMSUIPXCESECEWNWNWNWNWNWNLFC

kek2-ce05OS: RedHatWN(*): 48 (x8core)Memory: 4GB/WN

VOMSkek2-ce01OS: RedHatWN(*): 2 (x8core) Memory: 4GB/WN*)Number of WNs used in this research.GRID performance*See talk by Pr. Sasaki on Tuesday

GRID performance*Full simulation including beamlineTime consumed until all jobs are finishedFractions of initialization times (physics in blue, geometry in red) and simulation times

PHYSICS-BIOLOGYGeant4-DNA

How can Geant4-DNA model radiation biology ?*Physics stagestep-by-step modelling of physical interactions of incoming & secondary ionising radiation with biological medium (liquid water)Physicochemistry/chemistry stage Radical species production Diffusion Mutual interactionsGeometry stageDNA strands, chromatin fibres, chromosomes, whole cell nucleus, cells for the prediction of damages resulting from direct and indirect hits Excited water molecules Ionised water molecules Solvated electronsBiology stage DIRECT DNA damagesBiology stage INDIRECT DNA damages (dominant @ low LET)t=0t=10-15st=10-6sFJPPL

Geometrical stage - 1*The FJPPL activity was focused on the geometrical stage of Geant4-DNAObjective : develop a cellular phantom including chromosome territories down to DNA basesDr C. Omachi (KEK) visited CENBG for a month in 2011Developed a realistic cellular phantom obtained from confocal microscopy of HaCat keratinocyte line, including an ellipsoid cytoplasm and voxellized nucleus

~20mImage of a keratinocyte (HaCaT/(H2B-GFP)Tg) nucleus

Geometrical stage - 2*Each voxel contains a chromatine fiber elementEach chromatine fiber element is made of 6 nucleosomeEach nucleosome has 2 DNA 100-base pair loopsDNA is in the B-DNA conformationThe B-DNA sequence follows the ratio 6:4 (A-T VS G-C)

Geometrical stage - 3*46 chromosomes are built from a random walk approachEach chromosome has a selectable overall shapeSphere, cylinder, box5.4x104 voxels46 chromosomes

Geometrical stage - 4*Geometrical model was extended to a skin-like tissueTop view of three layers of skin-like tissue. One layer consists 100 voxels with 100 x 100 x 10 micrometer m3 volume each. Each voxel contains one nucleus shown as a green sphere that includes the 46 choromosomes.

These results have been presented at the IBA 2011 conference

Update on Geant4-DNA developmentsNew physics models upcomingElastic scattering for light ions in liquid waterProton and hydrogen physics models for DNA material First time in a public MC codeMulti-combination With photon Physics (Standard, Livermore, Penelope)With other EM processes and modelsIn different regions and energy rangesIncluding atomic deexcitationPrototype for water radiolysis simulation was released in Dec. 2011 in Geant4A user advanced example (dnachemistry) is in preparationVariable density feature

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New visualization schemeOn behalf of

Satoshi Tanaka Ritsumeikan U., JapanKuoko Hasegawa Ritsumeikan U., JapanAkinori Tanaka Ashikaga Inst. Of Tech., Japan

Conventional opaque visualizationThe conventional schemes are not good at visualizing very complicated geometryTend to be fuzzy No clear imagesNeeds sorting of polygons Computing time is proportional to N log N N: num. of polygonsArtifact because of failure of sortingIt is impossible to visualize opaquely polygon data, volume data and line data at the same time*

Latest scheme based on point-base rendering methodGroups of 3-D points allows very high precise visualization opaquelySorting operations are not necessary because of a stochastic algorithm This solved the problems coming from sort operations in conventional schemes Polygon data, volume data and line data can be visualized simultaneously Will be applicable for visualizing DNA structure also*

ATLAS*

ATLAS*

Dose*

Dose*

Geant4 Example*

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PARALLEL Geant4

Efforts toward parallel Geant4Computation speed of Geant4 is a big issue in many application fieldsHEP, medical, space, etc. In parallel, the computer industry is going to many-core CPUIntegration of accelerator chips on CPU will be soon availableIntel and NVIDIA*

Trends of CPUMany cores10 or more cores / CPUIntel MIC (pronounced like Mike)50 or more simplified x86 coresTo be available in 2012 as a PCI-e cardWill be integrated with CPU (2015 ?)Solve the bus neckNVIDIA ARM and GPGPU will be integratedSolve the bus neckARM is a CPU mostly used for mobile devices

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Cost effects Case of Belle II experiment at super B factory at KEKneeds 40 000 cores needed for MC productionYou may guess how much we can save if we speed up Geant4Much to do

Belle II CPU requirement provided by Prof. Hara. 1 CPU is almost 10 HEPSpec

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PROPOSED WORKPLAN

Workplan - 1*The KEK & CENBG teams met at IN2P3 headquarters on March 12, 2012 in Paris

3 main activities

Activity 1: Physics-MedicineContinue effort of validation of Geant4 physics processes for hadrontherapyPTSim will be extended to upcoming new Japanese facilitiesPromotion of PTSim in France

Workplan - 2*Activity 2 : Physics-Biology

Finalize the development & publication of Dr C. Omachis et al. cellular phantom model including DNA bases up to chromosome territories Dr C. Omachi got a new position at new Nagoyas protontherapy centerWill be performed by Dr Hirano (NIRS, Japan)Make it available as a Geant4 public example

Workplan - 3*Activity 3 : parallel Geant4Re-design of Geant4 kernel will be doneGeant4 collaboration wide discussion is necessaryOnly EM will be processed in parallel We forget hadronic interactions for a whileA toy model will be implemented A start point for the discussion

OutreachGeant4 & Geant4-DNA tutorialMuch interest in understanding biological effects of radiation at the cellular scale after the nuclear accident at FukushimaJapanese team deeply involved the Geant4/GATE tutorial at KISTI in Seoul, Oct. 31 Nov. 4, 2011Continue this common teaching effort between Japan, Korea and France

COLLABORATION MATTERS

Participants*

FranceJapanV. BretonLPC ClermontK. AmakoKEKC. ChampionU. Metz / CENBGT. AsoTNCMTS. EllesLAPPY. HiranoNIRSS. IncertiCENBGG. IwaiKEKJ. JacquemierLAPPA. KimuraAshikaga ITL. MaigneLPC ClermontK. MurakamiKEKI. MoreauCENBGC. OmachiNagoya cityY. PerrotLPC ClermontT. SasakiKEKC. SeznecCENBGS. TanakaRitsumeikan U.M. VerderiLLRH. YoshidaShikoku U.

Budget request for 2012*Request from FranceVisit CENBG team to KEK & NIRSend of summer 2012Possibly participate to a Geant4 tutorial

Request from Japan3 japanese visits to CENBG

Thank you very much*

**The PTSim was developed under the project Development... radio-therapy. The project itself have been funded by the JST CREST during 2003-2010. It may be a first project which was organized as a joint project among Geant4 developers, physicists, and medical physicists. We sampled use cases from medical physicists at the treatment facilities and developed a software suite for simulating particle therapy. The each category is highly modularized, so that many of them are imported into current GEANT4 distribution. *